"""
将鉴定到的SV信息转换成VCF文件
Example：
#reference      ref_start       ref_stop        ID      size    strand  type    ref_gap_size    query_gap_size  query_coordinates       method
1       797667  797723  Assemblytics_w_1        56      +       Deletion        56      0       chr1:1057443-1057443:+  within_alignment
1       2370620 2370694 Assemblytics_w_2        74      +       Deletion        74      0       chr1:2618601-2618601:+  within_alignment
1       2415323 2415378 Assemblytics_w_3        55      +       Deletion        55      0       chr1:2634724-2634724:+  within_alignment
1       2990378 2990438 Assemblytics_w_4        60      +       Deletion        60      0       chr1:3204701-3204701:+  within_alignment
1       2990685 2990685 Assemblytics_w_5        67      +       Insertion       0       67      chr1:3204949-3205016:+  within_alignment
1       3282782 3282858 Assemblytics_w_6        76      +       Deletion        76      0       chr1:3508331-3508331:+  within_alignment
1       3533593 3533593 Assemblytics_w_7        67      +       Insertion       0       67      chr1:3816656-3816723:+  within_alignment
1       7639753 7639815 Assemblytics_w_8        62      +       Deletion        62      0       chr1:7895784-7895784:+  within_alignment
1       8176397 8176397 Assemblytics_w_9        81      +       Insertion       0       81      chr1:8719150-8719231:+  within_alignment
1       8299090 8299090 Assemblytics_w_10       55      +       Insertion       0       55      chr1:9260231-9260286:+  within_alignment
1       9095617 9095683 Assemblytics_w_11       66      +       Deletion        66      0       chr1:10183503-10183503:+        within_alignment

Steps:
1. 建立基因组索引
2. 生成bed文件
3. 提取序列数据
Deletion: 从B73基因组提取
Insertion: 从对应的其他基因组提取
"""
import sys
import pandas as pd

# 参数1：bed文件路径
# 参数2：
# Step1 生成bed文件用于从基因组提取序列

df = pd.read_csv(sys.argv[1], sep='\t')



